DE performance

Performance of test function

Searches for the matrix with the higher probability of having a CGCGCG primer (only one solution). Minimizes 1-p(CGCGCG)

test.perf <- read.csv('~/mnt/edann/hexamers/strand_specific/test_function.performance.csv', header = FALSE, col.names = c('it','score'))
head(test.perf)

Test of real function

Functions for reshaping and plotting are in DE_performance.r

max(long.mat$iter)

[1] "999"

l <- lapply(seq(1,3), function(i) plot.iteration(long.mat, i))
# png('~/AvOwork/output/DE_optimization/test_iter_matrix.png')
for(el in l){
  # png(paste0("~/AvOwork/output/DE_optimization/DE_iter-", el$data$iter[1], ".png"))
  plot(el)
  # dev.off()
}

MIN RHO OF DIFFERENT TESTS

With bigger population size I get better scores and if the algorithm gets stuck in a local minimum it happens after more iterations.

rho.files.10 <- list.files(opt.dir, pattern='_pop10_its300.DE.rho.txt', full.names = TRUE)
rho.files.20 <- list.files(opt.dir, pattern='_pop20_its300.DE.rho.txt', full.names = TRUE)
rho.files.30 <- list.files(opt.dir, pattern='_pop30_its300.DE.rho.txt', full.names = TRUE)
plot.optimization.score(rho.files.10) +
  ggtitle('Pop.size=10')

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plot.optimization.score(rho.files.20) +
  ggtitle('Pop.size=20')

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plot.optimization.score(rho.files.30) +
  ggtitle('Pop.size=30')

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Test on new optimization: maximizing density in region of interest

plot.optimization.score(score.ctcf.files) 

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performance.mat <- read.csv(matrix.ctcf.files[4], row.names = 1)
long.mat <- reshape.prob.mat(performance.mat)

Using iter as id variables

head(performance.mat)

nrow(performance.mat)

[1] 100

lapply(matrix.ctcf.files, function(mat) 
  plot.iteration(reshape.prob.mat(read.csv(mat, row.names = 1)),99) +
    ggtitle(gsub(mat, pattern = '.+//', replacement = '')))

Using iter as id variables
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Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables

[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

[[10]]

Test4 is so weird! Best score and ends with all Ts!!

performance.mat <- read.csv(matrix.ctcf.files[5], row.names = 1)
long.mat <- reshape.prob.mat(performance.mat)
lapply(c(1,10,20,50,70,99),function(it) plot.iteration(long.mat, it))

What does the profile full of Ts look like?

bestmat.bw <- import(bestmat.bw.file, format = 'BigWig')

Error in import(bestmat.bw.file, format = "BigWig") : 
  could not find function "import"

Average coverage on CTCF sites

plot.refpoint.profile.df(not.norm.bestmat.df)

[1]   0 300 600

plot.refpoint.profile.df(norm.bestmat.df)

[1]   0 300 600

Optimizing density of enriched kmers

Not total abundance

1. Popsize = 20

plot.optimization.score(score.ctcf.files) +
  theme(legend.title = element_blank())

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2. Popsize = 30, 100 iterations

plot.optimization.score(score.ctcf.files) +
  theme(legend.title = element_blank())

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2. Popsize = 30, 100 iterations

plot.optimization.score(score.ctcf.files) +
  theme(legend.title = element_blank())

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Load coverage profiles around CTCF sites

prof.files <- list.files(paste0(opt.dir,'predicted_cov_bestmat'), pattern = 'profile.txt', full.names = T)
profiles <- lapply(prof.files, load.profile)

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names(profiles) <- gsub(prof.files, pattern = '.+500reg|.bestMat.+profile.txt', replacement = '')
df <- make.df.of.profiles(profiles)
best.scores <- sapply(score.ctcf.files, function(x) rev.default(scan(x))[1])

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names(best.scores) <- gsub(names(best.scores), pattern = '.+/|.DE.+.txt', replacement = '')
df.wScores <- df %>% mutate(score=best.scores[match(df$sample, names(best.scores))])
df.wScores %>% 
  filter(sample!='test1_ctcf_kmersFC_pop30_its100') %>% 
  filter(sample!="test10_ctcf_kmersFC_pop30_its100") %>% 
  plot.refpoint.profile.df(., color = 'score') +
  guides(color = guide_colorbar(barwidth = 20, barheight = 1))

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Not normalized

profiles <- lapply(prof.files, load.profile, normalize=F)

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names(profiles) <- gsub(prof.files, pattern = '.+500reg|.bestMat.+profile.txt', replacement = '')
df <- make.df.of.profiles(profiles)
best.scores <- sapply(score.ctcf.files, function(x) rev.default(scan(x))[1])

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names(best.scores) <- gsub(names(best.scores), pattern = '.+/|.DE.+.txt', replacement = '')
df.wScores <- df %>% mutate(score=best.scores[match(df$sample, names(best.scores))])
df.wScores %>% 
  filter(sample!='test1_ctcf_kmersFC_pop30_its100') %>% 
  filter(sample!="test10_ctcf_kmersFC_pop30_its100") %>% 
  plot.refpoint.profile.df(., color = 'score') +
  guides(color = guide_colorbar(barwidth = 20, barheight = 1))

[1]   0 300 600

Look at the coverage profiles in a set of regions for the best matrixes

plot.expVSpred.coverage.track(l.best.bw[[2]])

The following non-numeric data column has been dropped: id

[[1]]
Genome axis 'Axis'

[[2]]
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 4999
| samples:1
| strand: * 

regionsWctcf

 [1] "chr1 (1.82535e+08,1.8269e+08]"  "chr10 (8.91e+06,9.78e+06]"      "chr11 (7.0175e+07,7.032e+07]"   "chr13 (5.801e+07,5.816e+07]"   
 [5] "chr13 (9.9375e+07,9.9725e+07]"  "chr14 (2.1045e+07,2.111e+07]"   "chr14 (6.985e+07,6.989e+07]"    "chr15 (5.847e+07,5.878e+07]"   
 [9] "chr17 (2.6425e+07,2.6595e+07]"  "chr17 (2.776e+07,2.8335e+07]"   "chr17 (2.776e+07,2.8335e+07]"   "chr18 (6.0855e+07,6.1005e+07]" 
[13] "chr18 (6.4525e+07,6.461e+07]"   "chr18 (6.727e+07,6.7355e+07]"   "chr19 (3.2715e+07,3.305e+07]"   "chr19 (4.366e+07,4.4e+07]"     
[17] "chr2 (1.2636e+08,1.26775e+08]"  "chr2 (1.5342e+08,1.53505e+08]"  "chr4 (9.78e+06,9.88e+06]"       "chr6 (3.416e+07,3.426e+07]"    
[21] "chr6 (8.3135e+07,8.323e+07]"    "chr6 (1.48705e+08,1.49265e+08]" "chr7 (2.524e+07,2.552e+07]"     "chr7 (2.8335e+07,2.946e+07]"   
[25] "chr7 (2.8335e+07,2.946e+07]"    "chr7 (9.7675e+07,9.8015e+07]"   "chr7 (1.4244e+08,1.4268e+08]"   "chr8 (2.4525e+07,2.481e+07]"   
[29] "chr8 (5.366e+07,5.367e+07]"     "chr8 (8.4695e+07,8.47e+07]"     "chr8 (8.4695e+07,8.47e+07]"     "chr8 (1.0857e+08,1.08725e+08]" 
[33] "chr9 (1.06345e+08,1.06605e+08]" "chrX (1.53505e+08,1.5367e+08]" 

lapply(sample(regionsWctcf,10), function(x) plot.cov.wAnnotation(l.best.bw[x][[1]], ctcf))

The following non-numeric data column has been dropped: id

[[1]]
[[1]]$Axis
Genome axis 'Axis'

[[1]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 5000
| samples:1
| strand: * 

[[1]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr1
| annotation features: 1

[[1]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[2]]
[[2]]$Axis
Genome axis 'Axis'

[[2]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr19
| positions: 4999
| samples:1
| strand: * 

[[2]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr19
| annotation features: 1

[[2]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[3]]
[[3]]$Axis
Genome axis 'Axis'

[[3]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:1
| strand: * 

[[3]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 2

[[3]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[4]]
[[4]]$Axis
Genome axis 'Axis'

[[4]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr14
| positions: 4999
| samples:1
| strand: * 

[[4]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr14
| annotation features: 1

[[4]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[5]]
[[5]]$Axis
Genome axis 'Axis'

[[5]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr17
| positions: 4999
| samples:1
| strand: * 

[[5]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr17
| annotation features: 2

[[5]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[6]]
[[6]]$Axis
Genome axis 'Axis'

[[6]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:1
| strand: * 

[[6]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 2

[[6]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[7]]
[[7]]$Axis
Genome axis 'Axis'

[[7]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr13
| positions: 4999
| samples:1
| strand: * 

[[7]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr13
| annotation features: 1

[[7]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[8]]
[[8]]$Axis
Genome axis 'Axis'

[[8]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr18
| positions: 4999
| samples:1
| strand: * 

[[8]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr18
| annotation features: 1

[[8]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[9]]
[[9]]$Axis
Genome axis 'Axis'

[[9]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr17
| positions: 4999
| samples:1
| strand: * 

[[9]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr17
| annotation features: 2

[[9]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[10]]
[[10]]$Axis
Genome axis 'Axis'

[[10]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:1
| strand: * 

[[10]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 2

[[10]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 

Compare with even primer probability predicted coverage

plot.expVSpred.coverage.track(l.comon.bw[[2]])

The following non-numeric data column has been dropped: id

[[1]]
Genome axis 'Axis'

[[2]]
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 4999
| samples:2
| strand: * 

lapply(sample(regionsWctcf,10), function(x) plot.cov.wAnnotation(l.comon.bw[x][[1]], ctcf))

The following non-numeric data column has been dropped: id

[[1]]
[[1]]$Axis
Genome axis 'Axis'

[[1]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:2
| strand: * 

[[1]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 1

[[1]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[2]]
[[2]]$Axis
Genome axis 'Axis'

[[2]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr19
| positions: 4999
| samples:2
| strand: * 

[[2]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr19
| annotation features: 1

[[2]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[3]]
[[3]]$Axis
Genome axis 'Axis'

[[3]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:2
| strand: * 

[[3]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 1

[[3]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[4]]
[[4]]$Axis
Genome axis 'Axis'

[[4]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:2
| strand: * 

[[4]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 1

[[4]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[5]]
[[5]]$Axis
Genome axis 'Axis'

[[5]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:2
| strand: * 

[[5]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 2

[[5]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[6]]
[[6]]$Axis
Genome axis 'Axis'

[[6]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr18
| positions: 4999
| samples:2
| strand: * 

[[6]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr18
| annotation features: 1

[[6]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[7]]
[[7]]$Axis
Genome axis 'Axis'

[[7]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr6
| positions: 4999
| samples:2
| strand: * 

[[7]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr6
| annotation features: 1

[[7]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[8]]
[[8]]$Axis
Genome axis 'Axis'

[[8]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr2
| positions: 5000
| samples:2
| strand: * 

[[8]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr2
| annotation features: 1

[[8]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[9]]
[[9]]$Axis
Genome axis 'Axis'

[[9]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr4
| positions: 4999
| samples:2
| strand: * 

[[9]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr4
| annotation features: 1

[[9]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 




[[10]]
[[10]]$Axis
Genome axis 'Axis'

[[10]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 5000
| samples:2
| strand: * 

[[10]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr1
| annotation features: 1

[[10]]$titles
An object of class "ImageMap"
Slot "coords":
               x1        y1       x2        y2
Axis            6  37.24747 38.42335  77.20723
norm. coverage  6  77.20723 38.42335 278.26342
CTCF            6 278.26342 38.42335 318.47466

Slot "tags":
$title
            Axis   norm. coverage             CTCF 
          "Axis" "norm. coverage"           "CTCF" 

plot.refpoint.profile.df(df)

[1]   0 300 600

But here I am comparing noisy data (500 regions) and not noisy data (5000 regions)

EVEN COVERAGE

plot.optimization.score(score.even.files) +
  theme(legend.title = element_blank())

Read 100 items
Read 100 items
Read 100 items
Read 100 items
Read 100 items
Read 100 items

Variability in the initial population

Doesn’t seem to play a major role.

Visualizing in another way

Nope.